The utility of a phylogenetic marker can be described by its relative evolutionary rate (RER):faster (respectively slower) evolving markers will be more suitable for lower (respectively deeper) taxonomic levels.

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In a first approximation, the total branch length (TBL) of the maximum likelihood (ML) tree is a reasonable descriptor of the evolutionary rate of a given exon. However, the TBL will preclude fair comparisons among different exons when the taxon sampling differs: the higher the species number, the longer the TBL.

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To circumvent this problem, we use the Super Distance Matrix (SDM) approach [Criscuolo et al. 2006], with a three-step procedure:

(i) The ML tree inferred from each of the exons / CDS is converted into a matrix of additive distances by computing the path-length between each pair of species.

(ii) Each of the matrices is brought closer to the others by a factor (αp), according to the least-squares criterion. This operation is equivalent to multiplying by αp every branch length of the initial trees.

(iii) Optimal values of the alpha_p parameters are calculated following Criscuolo et al. (2006). As αp are inversely proportional to the evolutionary rates, 1/αp values provide a measure of rate heterogeneities among exons / CDS even if the number of taxa differs. Here, relative evolutionary rate SDM estimates range from 0.01 to 5 (OrthoMaM mean = 1.2 ; standard-error = 0.6).For example, if exons / CDSs X and Y are respectively characterized by relative rates rX = 0.2 and rY = 2.0, this means that Y is evolving 10 times faster than X.